Large differences among Giardia isolates were noted. 18S rDNA sequence differences were detected among isolates but were identical among the same Giardia Group. Comparison of the triosphophate isomerase genes of two isolates known to differ from each other by other criteria revealed a 19% sequence difference which resulted in a 9% amino acid divergence. A transcript was identified, sequenced and characterized. It was transcribed in only one of three Groups of Giardia and therefore is a unique marker of this group. The genomic organization of the VSP genes can differ among isolates.